rs7872903

Variant names:

• chr9-133619170-T-C
• rs7872903
• ENST00000564021.1:n.114-5496A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000564021.1(ENSG00000261018):​n.114-5496A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,142 control chromosomes in the GnomAD database, including 7,377 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (7377 hom., cov: 32)
• Consequence: ENSG00000261018 ENST00000564021.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

Genes affected

ENSG00000261018 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261018	ENST00000564021.1	n.114-5496A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41930 AN: 152024 Hom.: 7360 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.00982

Gnomad SAS AF: 0.0551

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.247

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.276 AC: 41979 AN: 152142 Hom.: 7377 Cov.: 32 AF XY: 0.265 AC XY: 19698 AN XY: 74384

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.00965

Gnomad4 SAS AF: 0.0545

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.244

Alfa AF: 0.225 Hom.: 5788

Bravo AF: 0.284

Asia WGS AF: 0.0760 AC: 267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.1
DANN	Benign	0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7872903; hg19: chr9-136484292;